rs3891355

chr12-106556917-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_040246.1(LOC100287944):n.143-49107A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,062 control chromosomes in the GnomAD database, including 1,312 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (1312 hom., cov: 32)
• Consequence: LOC100287944 NR_040246.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100287944	NR_040246.1	n.143-49107A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000551505.4	n.230-56735A>G		intron_variant, non_coding_transcript_variant		4
	ENST00000549203.2	n.143-49107A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18735 AN: 151944 Hom.: 1314 Cov.: 32

Gnomad AFR AF: 0.0719

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0641

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.118

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.123 AC: 18727 AN: 152062 Hom.: 1312 Cov.: 32 AF XY: 0.122 AC XY: 9079 AN XY: 74300

Gnomad4 AFR AF: 0.0719

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0622

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.117

Alfa AF: 0.145 Hom.: 3647

Bravo AF: 0.115

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.8
Dann	Benign	0.68

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3891355; hg19: chr12-106950695;